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Series GSE53840 Query DataSets for GSE53840
Status Public on Nov 03, 2014
Title Whole blood DNA methylation samples from HIV positive men [2013 study]
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Genome wide DNA methylation profiles of whole blood from HIV positive men. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 120 subjects from the USA but because of missing clinical characteristics only 109 subjects were used in the scientific publication. The study analyzed the effect of HIV viral load on host DNA methylation levels.
Overall design Bisulphite converted DNA from the 120 HIV positive men were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Subjects had different levels of HIV viral load.

This dataset reports DNA methylation data set on 120 subjects that were generated in 2013 (while the other data set of 24 subjects reports DNA methylation data generated in 2012).

Details on what each sample characteristics and their values represent are provided in the 'characteristics_readme.txt' file.

Please cite PMID: 25969563.
Contributor(s) Horvath S, Levine AJ
Citation(s) 25313081, 25969563
Submission date Jan 06, 2014
Last update date Mar 22, 2019
Contact name Steve Horvath
Organization name University of California, Los Angeles
Department Human Genetics
Lab Horvath
Street address 695 Charles E. Young Drive South, Box 708822
City Los Angeles
State/province CA
ZIP/Postal code 90095-7088
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (120)
GSM1301871 genomic DNA from whole blood of HIV+ man 1
GSM1301872 genomic DNA from whole blood of HIV+ man 2
GSM1301873 genomic DNA from whole blood of HIV+ man 3
BioProject PRJNA233508

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE53840_RAW.tar 183.1 Mb (http)(custom) TAR
GSE53840_characteristics_readme.txt 3.0 Kb (ftp)(http) TXT
GSE53840_non_normalized.txt.gz 271.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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